[maker-devel] Question on BLAST/Gbrowse

[Barry Moore]

Shane,

NCBI distributes (or at least used to - I haven't looked in a while) a  
version of their BLAST which runs as a webserver.  I think you can  
customize the links, so it's possible you could run that as the blast  
server, and then have the links point to you GBrowse URLs.  If  that's  
direction doesn't look promising, I've done similar things - having  
blast results link to database info pages using Bioperl's  
Bio::SearchIO::Writer HTMLResultWriter.  Intercept the blast output,  
in inject the URL's you want before using the above module to print it  
out in a format that will be fairly similar to the original blast  
report output.

Barry

On Oct 5, 2009, at 12:49 PM, Shane Brubaker wrote:

> Hi, I’m sorry if this is not directly related to MAKER, but I was  
> wondering if anyone knows of a product for setting up a BLAST web  
> site that then gives you links to scaffolds/annotations that are in  
> GBrowser (from MAKER).
>
> We have a genome with a bunch of scaffolds, and it is unlikely  
> someone would want to browse through them.  Instead the scientists  
> want to blast a gene and then get a link to that scaffold/location.
>
> Is there any open source code out there for doing this?
>
>
> Thanks,
> Shane
>
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